Using Waystones_1.12.2-4.0.67, in gamemode 1 on a Survival server, everytime I place a Waystone, it ask for settings, I set, but it is ALWAYS Random Name, without Global

Are you running any other mods? I tried reproducing this but could not. I tested on both integrated and dedicated servers, with survival-type worlds.

Are you pressing the "done" button? If you press escape, it will not save the settings.

Yeah, sorry for that, I was tired, sick and frustrated that this stopped working.
Quick test, culprit is Atlas Extra
Will report to them